id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 20311 Match→Align associating to alignment: numpy error chimerax-bug-report@… Eric Pettersen "{{{ The following bug report has been submitted: Platform: macOS-14.8.3-x86_64-i386-64bit ChimeraX Version: 1.12rc202605070126 (2026-05-07 01:26:37 UTC) Description ui tool show Match→Align msa3d #2/A#3/A Match→Align cutoff: 5.0, in column if within cutoff of: any 82 residue pairs aligned 110 fully populated columns Pairwise RMSDs across all fully populated columns Model 2 3 2 0.000 28.811 3 28.811 0.000 Overall RMSD: 28.811 Sequence lengths: 110 522 SDM (cutoff 5.0): -247.145 Q-score: 0.002 Alignment identifier is MA-1 Showing conservation header (""seq_clustal_conservation"" residue attribute) for alignment MA-1 Traceback (most recent call last): File ""/Applications/ChimeraX-1.12-rc2026.05.07.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/match_align/tool.py"", line 259, in match_align run(self.session, ""msa3d "" + ' '.join(args)) File ""/Applications/ChimeraX-1.12-rc2026.05.07.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/run.py"", line 49, in run results = command.run(text, log=log, return_json=return_json) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/Applications/ChimeraX-1.12-rc2026.05.07.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/cli.py"", line 3245, in run result = ci.function(session, **kw_args) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/Applications/ChimeraX-1.12-rc2026.05.07.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/match_align/cmd.py"", line 225, in make_alignment alignment.associate(orig, seq=aligned, silent=True) File ""/Applications/ChimeraX-1.12-rc2026.05.07.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/seqalign/alignment.py"", line 386, in associate do_assoc() File ""/Applications/ChimeraX-1.12-rc2026.05.07.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/seqalign/alignment.py"", line 305, in do_assoc self.prematched_assoc_structure(best_match_map, best_errors, reassoc) File ""/Applications/ChimeraX-1.12-rc2026.05.07.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/seqalign/alignment.py"", line 742, in prematched_assoc_structure self._set_residue_attributes(match_maps=[match_map]) File ""/Applications/ChimeraX-1.12-rc2026.05.07.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/seqalign/alignment.py"", line 1071, in _set_residue_attributes values = [100.0 * self.most_common(col)[1] / num_seqs for col in range(len(self._seqs[0]))] ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/Applications/ChimeraX-1.12-rc2026.05.07.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/seqalign/alignment.py"", line 1071, in values = [100.0 * self.most_common(col)[1] / num_seqs for col in range(len(self._seqs[0]))] ^^^^^^^^^^^^^^^^^^^^^ File ""/Applications/ChimeraX-1.12-rc2026.05.07.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/seqalign/alignment.py"", line 691, in most_common chars, counts = self.column_counts()[col_index] ^^^^^^^^^^^^^^^^^^^^ File ""/Applications/ChimeraX-1.12-rc2026.05.07.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/seqalign/alignment.py"", line 485, in column_counts data = numpy.array([list(seq.characters) for seq in self._seqs]) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ ValueError: setting an array element with a sequence. The requested array has an inhomogeneous shape after 1 dimensions. The detected shape was (2,) + inhomogeneous part. ValueError: setting an array element with a sequence. The requested array has an inhomogeneous shape after 1 dimensions. The detected shape was (2,) + inhomogeneous part. File ""/Applications/ChimeraX-1.12-rc2026.05.07.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/seqalign/alignment.py"", line 485, in column_counts data = numpy.array([list(seq.characters) for seq in self._seqs]) Log: UCSF ChimeraX version: 1.12rc202605070126 (2026-05-07) © 2016-2026 Regents of the University of California. All rights reserved. > open ""/Users/frankseeber/Documents/RKI/2nd LEA paper/850His/850His vs > 860His_1.cxs"" Log from Sun Jan 25 11:55:12 2026UCSF ChimeraX version: 1.11 (2025-12-17) © 2016-2025 Regents of the University of California. All rights reserved. > open ""/Users/frankseeber/Documents/RKI/2nd LEA paper/850His/850His vs > 860His_1.cxs"" Log from Sun Jan 25 11:18:21 2026UCSF ChimeraX version: 1.11 (2025-12-17) © 2016-2025 Regents of the University of California. All rights reserved. > open ""/Users/frankseeber/Documents/RKI/2nd LEA paper/850His/850His vs > 860His.cxs"" format session Log from Tue Jan 20 17:12:49 2026UCSF ChimeraX version: 1.11 (2025-12-17) © 2016-2025 Regents of the University of California. All rights reserved. > open ""/Users/frankseeber/Documents/RKI/2nd LEA paper/850His/850His vs > 860His.cxs"" format session Log from Tue Jan 20 16:53:43 2026UCSF ChimeraX version: 1.11 (2025-12-17) © 2016-2025 Regents of the University of California. All rights reserved. > open ""/Users/frankseeber/Documents/RKI/2nd LEA paper/850His/850His vs > 860His.cxs"" Log from Tue Jan 20 16:01:25 2026 > set bgColor light grey > ui tool show ""command line interface"" UCSF ChimeraX version: 1.11 (2025-12-17) © 2016-2025 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open /Users/frankseeber/Downloads/6His-860/6His-860_0.cif format mmcif 6His-860_0.cif title: Chai-1 predicted structure [more info...] Chain information for 6His-860_0.cif #1 --- Chain | Description A | Entity A Color 6His-860_0.cif by residue attribute pLDDT_score Computing secondary structure > close session > open ""/Users/frankseeber/Documents/RKI/2nd LEA paper/850His/850His_0.cif"" > format mmcif 850His_0.cif title: Chai-1 predicted structure [more info...] Chain information for 850His_0.cif #1 --- Chain | Description A | Entity A Color 850His_0.cif by residue attribute pLDDT_score Computing secondary structure > open ""/Users/frankseeber/Documents/RKI/2nd LEA paper/850His/850His_0.cif"" > format mmcif 850His_0.cif title: Chai-1 predicted structure [more info...] Chain information for 850His_0.cif #2 --- Chain | Description A | Entity A Color 850His_0.cif by residue attribute pLDDT_score Computing secondary structure > open /Users/frankseeber/Downloads/6His-860/6His-860_0.cif 6His-860_0.cif title: Chai-1 predicted structure [more info...] Chain information for 6His-860_0.cif #3 --- Chain | Description A | Entity A Color 6His-860_0.cif by residue attribute pLDDT_score Computing secondary structure > ui tool show Matchmaker > close #1 > ui tool show Matchmaker > matchmaker #3 to #2 Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker 850His_0.cif, chain A (#2) with 6His-860_0.cif, chain A (#3), sequence alignment score = 152.3 RMSD between 50 pruned atom pairs is 1.232 angstroms; (across all 105 pairs: 14.240) > ui tool show Matchmaker > matchmaker #3 to #2 showAlignment true Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker 850His_0.cif, chain A (#2) with 6His-860_0.cif, chain A (#3), sequence alignment score = 152.3 Alignment identifier is 1 Showing conservation header (""seq_clustal_conservation"" residue attribute) for alignment 1 Hiding conservation header for alignment 1 Chains used in RMSD evaluation for alignment 1: 850His_0.cif #2/A, 6His-860_0.cif #3/A Showing rmsd header (""seq_rmsd"" residue attribute) for alignment 1 RMSD between 50 pruned atom pairs is 1.232 angstroms; (across all 105 pairs: 14.240) > cd ""/Users/frankseeber/Documents/RKI/2nd LEA paper/850His"" Current working directory is: /Users/frankseeber/Documents/RKI/2nd LEA paper/850His > save ""/Users/frankseeber/Documents/RKI/2nd LEA paper/850His/850His vs > 860His.cxs"" ——— End of log from Tue Jan 20 16:01:25 2026 ——— > view name session-start opened ChimeraX session > select #3/a:1-177,259-525 3365 atoms, 3419 bonds, 441 residues, 1 model selected > color sel #c0c0c0ff [Repeated 1 time(s)] > color sel #c0c0c0fa > color sel #c0c0c0e5 > color sel #c0c0c0d5 > color sel #c0c0c0cf > color sel #c0c0c0cc > color sel #c0c0c0c7 > color sel #c0c0c0b8 > set bgColor white > color sel #c0c0c0b6 > color sel #c0c0c0ac > color sel #c0c0c0a9 > color sel #c0c0c09b > color sel #c0c0c099 > color sel #c0c0c094 > color sel #c0c0c092 > color sel #c0c0c091 > color sel #c0c0c08f > color sel #c0c0c08b > color sel #c0c0c08a > color sel #c0c0c088 > color sel #c0c0c081 > color sel #c0c0c079 > color sel #c0c0c072 > color sel #c0c0c071 > color sel #c0c0c0ff > color sel #ebebebff > color sel #d6d6d6ff > color sel #ebebebff > color sel #d6d6d6ff > select clear > select #3/a:1-177,259-525 3365 atoms, 3419 bonds, 441 residues, 1 model selected > color sel #d6d6d6ff > color sel #d6d6d6f7 > color sel #d6d6d6ec > color sel #d6d6d6ea > color sel #d6d6d6cb > color sel #d6d6d6b1 > color sel #d6d6d6a9 > color sel #d6d6d694 > color sel #d6d6d686 > color sel #d6d6d67d > color sel #d6d6d67b > color sel #d6d6d678 > color sel #d6d6d66e > color sel #d6d6d661 > color sel #d6d6d65a [Repeated 1 time(s)] > color sel #d6d6d66a > color sel #d6d6d672 > color sel #d6d6d67e > color sel #d6d6d687 > color sel #d6d6d693 > color sel #d6d6d695 > color sel #d6d6d697 > color sel #d6d6d698 > color sel #d6d6d656 > color sel #d6d6d615 > color sel #d6d6d604 > color sel #d6d6d600 > color sel #d6d6d611 > color sel #d6d6d635 > color sel #d6d6d646 > color sel #d6d6d64a > color sel #d6d6d663 > color sel #d6d6d677 [Repeated 1 time(s)] > color sel #d6d6d663 > color sel #d6d6d60a > color sel #d6d6d600 > color sel #d6d6d60a > color sel #d6d6d62c > color sel #d6d6d632 > color sel #d6d6d631 > color sel #d6d6d62c > color sel #d6d6d628 > color sel #d6d6d626 [Repeated 1 time(s)] > color sel #d6d6d625 > color sel #d6d6d626 > color sel #d6d6d628 > color sel #d6d6d629 > color sel #d6d6d62a > color sel #d6d6d62e > color sel #d6d6d630 > color sel #d6d6d632 > color sel #d6d6d633 > color sel #d6d6d634 > color sel #d6d6d636 [Repeated 1 time(s)] > select clear > cd ""/Users/frankseeber/Documents/RKI/2nd LEA paper/850His"" Current working directory is: /Users/frankseeber/Documents/RKI/2nd LEA paper/850His > save ""/Users/frankseeber/Documents/RKI/2nd LEA paper/850His/850His vs > 860His.cxs"" [Repeated 1 time(s)] ——— End of log from Tue Jan 20 16:53:43 2026 ——— > view name session-start opened ChimeraX session > select #3/a:1-177,259-525 3365 atoms, 3419 bonds, 441 residues, 1 model selected > color sel #a9a9a942 > color sel #a9a9a944 > color sel #a9a9a947 > color sel #a9a9a948 > color sel #a9a9a949 > color sel #a9a9a94b > color sel #a9a9a94c > color sel #a9a9a94d > color sel #a9a9a94f > color sel #a9a9a950 > color sel #a9a9a952 > color sel #a9a9a953 > color sel #a9a9a954 > color sel #a9a9a955 > color sel #a9a9a956 > color sel #a9a9a958 [Repeated 1 time(s)] > color sel #a9a9a959 [Repeated 1 time(s)] > color sel #a9a9a95b > color sel #a9a9a95c > color sel #a9a9a95d [Repeated 1 time(s)] > color sel #a9a9a95e > select clear > cd ""/Users/frankseeber/Documents/RKI/2nd LEA paper/850His"" Current working directory is: /Users/frankseeber/Documents/RKI/2nd LEA paper/850His > save ""/Users/frankseeber/Documents/RKI/2nd LEA paper/850His/850His vs > 860His.cxs"" ——— End of log from Tue Jan 20 17:12:49 2026 ——— > view name session-start opened ChimeraX session > select #3/a:1-177,259-525 3365 atoms, 3419 bonds, 441 residues, 1 model selected > select #3/a:1-177,259-525 3365 atoms, 3419 bonds, 441 residues, 1 model selected > ""select #3/a:1-177,259-525"" Unknown command: ""select #3/a:1-177,259-525"" > select #3/a:1-177,259-525 3365 atoms, 3419 bonds, 441 residues, 1 model selected > select #3/a:1-525 3959 atoms, 4022 bonds, 522 residues, 1 model selected > color sel #ebebebff > select clear > select #3/a:1-177,259-525 3365 atoms, 3419 bonds, 441 residues, 1 model selected > select #3/a:181-260 586 atoms, 593 bonds, 80 residues, 1 model selected > color sel #dda0ddff > cd ""/Users/frankseeber/Documents/RKI/2nd LEA paper/850His/6His-860"" Current working directory is: /Users/frankseeber/Documents/RKI/2nd LEA paper/850His/6His-860 > save ""/Users/frankseeber/Documents/RKI/2nd LEA paper/850His/850His vs > 860His_1.cxs"" ——— End of log from Sun Jan 25 11:18:21 2026 ——— > view name session-start opened ChimeraX session > cd ""/Users/frankseeber/Documents/RKI/2nd LEA paper/850His"" Current working directory is: /Users/frankseeber/Documents/RKI/2nd LEA paper/850His > save ""/Users/frankseeber/Documents/RKI/2nd LEA paper/850His/850His vs > 860His_1.cxs"" > save /Users/frankseeber/Desktop/model_1.tif width 1800 transparentBackground > true [Repeated 3 time(s)] > save ""/Users/frankseeber/Documents/RKI/2nd LEA paper/850His/850His vs > 860His_1.cxs"" ——— End of log from Sun Jan 25 11:55:12 2026 ——— > view name session-start opened ChimeraX session > ui tool show ""Show Sequence Viewer"" > sequence chain #2/A Alignment identifier is 2/A > sequence chain #3/A Alignment identifier is 3/A > ui tool show Match→Align > msa3d #2/A#3/A Match→Align cutoff: 5.0, in column if within cutoff of: any 82 residue pairs aligned 110 fully populated columns Pairwise RMSDs across all fully populated columns --- Model | 2 | 3 2 | 0.000 | 28.811 3 | 28.811 | 0.000 Overall RMSD: 28.811 Sequence lengths: 110 522 SDM (cutoff 5.0): -247.145 Q-score: 0.002 Alignment identifier is MA-1 Showing conservation header (""seq_clustal_conservation"" residue attribute) for alignment MA-1 Traceback (most recent call last): File ""/Applications/ChimeraX-1.12-rc2026.05.07.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/match_align/tool.py"", line 259, in match_align run(self.session, ""msa3d "" + ' '.join(args)) File ""/Applications/ChimeraX-1.12-rc2026.05.07.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/core/commands/run.py"", line 49, in run results = command.run(text, log=log, return_json=return_json) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/Applications/ChimeraX-1.12-rc2026.05.07.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/core/commands/cli.py"", line 3245, in run result = ci.function(session, **kw_args) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/Applications/ChimeraX-1.12-rc2026.05.07.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/match_align/cmd.py"", line 225, in make_alignment alignment.associate(orig, seq=aligned, silent=True) File ""/Applications/ChimeraX-1.12-rc2026.05.07.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/seqalign/alignment.py"", line 386, in associate do_assoc() File ""/Applications/ChimeraX-1.12-rc2026.05.07.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/seqalign/alignment.py"", line 305, in do_assoc self.prematched_assoc_structure(best_match_map, best_errors, reassoc) File ""/Applications/ChimeraX-1.12-rc2026.05.07.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/seqalign/alignment.py"", line 742, in prematched_assoc_structure self._set_residue_attributes(match_maps=[match_map]) File ""/Applications/ChimeraX-1.12-rc2026.05.07.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/seqalign/alignment.py"", line 1071, in _set_residue_attributes values = [100.0 * self.most_common(col)[1] / num_seqs for col in range(len(self._seqs[0]))] ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/Applications/ChimeraX-1.12-rc2026.05.07.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/seqalign/alignment.py"", line 1071, in values = [100.0 * self.most_common(col)[1] / num_seqs for col in range(len(self._seqs[0]))] ^^^^^^^^^^^^^^^^^^^^^ File ""/Applications/ChimeraX-1.12-rc2026.05.07.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/seqalign/alignment.py"", line 691, in most_common chars, counts = self.column_counts()[col_index] ^^^^^^^^^^^^^^^^^^^^ File ""/Applications/ChimeraX-1.12-rc2026.05.07.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/seqalign/alignment.py"", line 485, in column_counts data = numpy.array([list(seq.characters) for seq in self._seqs]) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ ValueError: setting an array element with a sequence. The requested array has an inhomogeneous shape after 1 dimensions. The detected shape was (2,) + inhomogeneous part. ValueError: setting an array element with a sequence. The requested array has an inhomogeneous shape after 1 dimensions. The detected shape was (2,) + inhomogeneous part. File ""/Applications/ChimeraX-1.12-rc2026.05.07.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/seqalign/alignment.py"", line 485, in column_counts data = numpy.array([list(seq.characters) for seq in self._seqs]) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ See log for complete Python traceback. OpenGL version: 4.1 INTEL-22.5.15 OpenGL renderer: Intel(R) Iris(TM) Plus Graphics OpenGL Engine OpenGL vendor: Intel Inc. Python: 3.11.9 Locale: UTF-8 Qt version: PyQt6 6.10.2, Qt 6.10.0 Qt runtime version: 6.10.1 Qt platform: cocoa Hardware: Hardware Overview: Model Name: MacBook Pro Model Identifier: MacBookPro16,2 Processor Name: Quad-Core Intel Core i7 Processor Speed: 2,3 GHz Number of Processors: 1 Total Number of Cores: 4 L2 Cache (per Core): 512 KB L3 Cache: 8 MB Hyper-Threading Technology: Enabled Memory: 32 GB System Firmware Version: 2094.80.5.0.0 (iBridge: 23.16.13120.0.0,0) OS Loader Version: 580.140.1~106 Software: System Software Overview: System Version: macOS 14.8.3 (23J220) Kernel Version: Darwin 23.6.0 Time since boot: 4 Tage, 4 Stunden und 42 Minuten Graphics/Displays: Intel Iris Plus Graphics: Chipset Model: Intel Iris Plus Graphics Type: GPU Bus: Built-In VRAM (Dynamic, Max): 1536 MB Vendor: Intel Device ID: 0x8a53 Revision ID: 0x0007 Metal Support: Metal 3 Displays: Color LCD: Display Type: Built-In Retina LCD Resolution: 2560 x 1600 Retina Framebuffer Depth: 30-Bit Color (ARGB2101010) Mirror: Off Online: Yes Automatically Adjust Brightness: No Connection Type: Internal DELL U2421E: Resolution: 1920 x 1200 (WUXGA - Widescreen Ultra eXtended Graphics Array) UI Looks like: 1920 x 1200 @ 59.00Hz Framebuffer Depth: 30-Bit Color (ARGB2101010) Display Serial Number: 2S6N6H3 Mirror: Off Online: Yes Rotation: Supported Connection Type: Thunderbolt/DisplayPort DELL U2421E: Resolution: 1920 x 1200 (WUXGA - Widescreen Ultra eXtended Graphics Array) UI Looks like: 1920 x 1200 @ 59.00Hz Framebuffer Depth: 30-Bit Color (ARGB2101010) Display Serial Number: BPTJBH3 Main Display: Yes Mirror: Off Online: Yes Rotation: Supported Connection Type: Thunderbolt/DisplayPort Installed Packages: accessible-pygments: 0.0.5 aiohappyeyeballs: 2.6.1 aiohttp: 3.13.1 aiosignal: 1.4.0 alabaster: 1.0.0 annotated-types: 0.7.0 anyio: 4.13.0 appdirs: 1.4.4 appnope: 0.1.4 asttokens: 3.0.1 attrs: 26.1.0 babel: 2.18.0 beautifulsoup4: 4.13.5 blockdiag: 3.0.0 blosc2: 4.1.2 bs4: 0.0.2 build: 1.3.0 certifi: 2025.7.14 cftime: 1.6.5 charset-normalizer: 3.4.7 ChimeraX-AddCharge: 1.5.20 ChimeraX-AddH: 2.2.8 ChimeraX-AlignmentAlgorithms: 2.0.2 ChimeraX-AlignmentHdrs: 3.6.2 ChimeraX-AlignmentMatrices: 2.1 ChimeraX-Alignments: 3.2 ChimeraX-AlphaFold: 1.0.1 ChimeraX-AltlocExplorer: 1.2 ChimeraX-AmberInfo: 1.0 ChimeraX-Animations: 1.0 ChimeraX-Aniso: 1.3.2 ChimeraX-Arrays: 1.1 ChimeraX-Atomic: 1.67.1 ChimeraX-AtomicLibrary: 14.4 ChimeraX-AtomSearch: 2.0.1 ChimeraX-AxesPlanes: 2.4 ChimeraX-BasicActions: 1.1.3 ChimeraX-BILD: 1.0 ChimeraX-BlastProtein: 3.0.0 ChimeraX-Boltz: 1.1 ChimeraX-BondRot: 2.0.4 ChimeraX-BugReporter: 1.0.2 ChimeraX-BuildStructure: 2.13.1 ChimeraX-Bumps: 1.0 ChimeraX-BundleBuilder: 1.6.0 ChimeraX-ButtonPanel: 1.0.1 ChimeraX-CageBuilder: 1.0.1 ChimeraX-CellPack: 1.0 ChimeraX-Centroids: 1.4.1 ChimeraX-ChangeChains: 1.1 ChimeraX-CheckWaters: 1.5 ChimeraX-ChemGroup: 2.0.2 ChimeraX-Clashes: 2.4 ChimeraX-Cluster: 1.0 ChimeraX-ColorActions: 1.0.5 ChimeraX-ColorGlobe: 1.0 ChimeraX-ColorKey: 1.5.8 ChimeraX-CommandLine: 1.3.1 ChimeraX-ConnectStructure: 2.0.1 ChimeraX-Contacts: 1.0.1 ChimeraX-Core: 1.12rc202605070126 ChimeraX-CoreFormats: 1.2 ChimeraX-coulombic: 1.4.5 ChimeraX-Crosslinks: 1.0 ChimeraX-Crystal: 1.0 ChimeraX-CrystalContacts: 1.0.1 ChimeraX-DataFormats: 1.2.4 ChimeraX-Dicom: 1.2.7 ChimeraX-DistMonitor: 1.4.2 ChimeraX-DockPrep: 1.2.1 ChimeraX-Dssp: 2.0 ChimeraX-EMDB-SFF: 1.0 ChimeraX-ESMFold: 1.0 ChimeraX-FileHistory: 1.0.1 ChimeraX-FunctionKey: 1.0.1 ChimeraX-Geometry: 1.3 ChimeraX-gltf: 1.0 ChimeraX-Graphics: 1.4.1 ChimeraX-Hbonds: 2.5.3 ChimeraX-Help: 1.3 ChimeraX-HKCage: 1.3 ChimeraX-IHM: 1.1 ChimeraX-ImageFormats: 1.2 ChimeraX-IMOD: 1.0 ChimeraX-IO: 1.0.4 ChimeraX-ItemsInspection: 1.0.1 ChimeraX-IUPAC: 1.0 ChimeraX-KVFinder: 1.8.2 ChimeraX-Label: 1.5 ChimeraX-LightingGUI: 1.0 ChimeraX-ListInfo: 1.3.1 ChimeraX-Log: 1.2.2 ChimeraX-LookingGlass: 1.1 ChimeraX-Maestro: 1.9.3 ChimeraX-Map: 1.3 ChimeraX-MapData: 2.0 ChimeraX-MapEraser: 1.0.1 ChimeraX-MapFilter: 2.0.1 ChimeraX-MapFit: 2.0 ChimeraX-MapSeries: 2.1.1 ChimeraX-Markers: 1.0.1 ChimeraX-Mask: 1.0.2 ChimeraX-MatchAlign: 1.1 ChimeraX-MatchMaker: 2.4 ChimeraX-MCopy: 1.0 ChimeraX-MCPServer: 0.2.0 ChimeraX-MDcrds: 2.19 ChimeraX-MedicalToolbar: 1.1 ChimeraX-Meeting: 1.0.1 ChimeraX-Minimize: 1.3.8 ChimeraX-MLP: 1.1.1 ChimeraX-mmCIF: 2.16 ChimeraX-MMTF: 2.2 ChimeraX-ModelArchive: 1.0 ChimeraX-Modeller: 1.5.23 ChimeraX-ModelPanel: 1.6.1 ChimeraX-ModelSeries: 1.0.1 ChimeraX-Mol2: 2.0.3 ChimeraX-Mole: 1.0 ChimeraX-Morph: 1.0.2 ChimeraX-MouseModes: 1.2 ChimeraX-Movie: 1.0.1 ChimeraX-MutationScores: 1.0 ChimeraX-Neuron: 1.0 ChimeraX-Nifti: 1.2 ChimeraX-NMRSTAR: 1.0.2 ChimeraX-NRRD: 1.2 ChimeraX-Nucleotides: 2.0.3 ChimeraX-OpenCommand: 1.15.4 ChimeraX-OpenFold: 1.0 ChimeraX-OrthoPick: 1.0.1 ChimeraX-PDB: 2.7.13 ChimeraX-PDBBio: 1.0.1 ChimeraX-PDBLibrary: 1.0.5 ChimeraX-PDBMatrices: 1.0 ChimeraX-PickBlobs: 1.0.1 ChimeraX-Positions: 1.0 ChimeraX-PresetMgr: 1.1.4 ChimeraX-ProfileGrids: 1.6 ChimeraX-PubChem: 2.2 ChimeraX-ReadPbonds: 1.0.1 ChimeraX-Registration: 1.1.2 ChimeraX-RemoteControl: 1.0 ChimeraX-RenderByAttr: 1.8.2 ChimeraX-RenumberResidues: 1.1 ChimeraX-ResidueFit: 1.0.1 ChimeraX-RestServer: 1.3.3 ChimeraX-RNALayout: 1.0 ChimeraX-RotamerLibMgr: 4.0 ChimeraX-RotamerLibsDunbrack: 2.0 ChimeraX-RotamerLibsDynameomics: 2.0 ChimeraX-RotamerLibsRichardson: 2.0 ChimeraX-SaveCommand: 1.5.2 ChimeraX-Scenes: 0.3.1 ChimeraX-SchemeMgr: 1.0 ChimeraX-SDF: 2.0.3 ChimeraX-Segger: 1.0 ChimeraX-Segment: 1.0.1 ChimeraX-Segmentations: 3.5.12 ChimeraX-SelInspector: 1.0 ChimeraX-SeqView: 2.18 ChimeraX-Shape: 1.1 ChimeraX-Shell: 1.0.1 ChimeraX-Shortcuts: 1.2.1 ChimeraX-ShowSequences: 1.0.3 ChimeraX-SideView: 1.0.1 ChimeraX-SimilarStructures: 1.0.1 ChimeraX-Smiles: 2.1.2 ChimeraX-SmoothLines: 1.0 ChimeraX-SNFG: 1.0 ChimeraX-SpaceNavigator: 1.0 ChimeraX-StdCommands: 1.19.3 ChimeraX-STL: 1.0.1 ChimeraX-Storm: 1.0 ChimeraX-StructMeasure: 1.2.1 ChimeraX-Struts: 1.0.1 ChimeraX-Surface: 1.0.1 ChimeraX-SwapAA: 2.0.1 ChimeraX-SwapRes: 2.5.3 ChimeraX-TapeMeasure: 1.0 ChimeraX-TaskManager: 1.0 ChimeraX-Test: 1.0 ChimeraX-Toolbar: 1.2.4 ChimeraX-ToolshedUtils: 1.2.4 ChimeraX-Topography: 1.0 ChimeraX-ToQuest: 1.0 ChimeraX-Tug: 1.0.1 ChimeraX-UI: 1.50.6 ChimeraX-Umap: 1.0 ChimeraX-uniprot: 2.3.2 ChimeraX-UnitCell: 1.0.1 ChimeraX-ViewDock: 1.6.2 ChimeraX-VIPERdb: 1.0 ChimeraX-Vive: 1.1 ChimeraX-VolumeMenu: 1.0.1 ChimeraX-vrml: 1.0 ChimeraX-VTK: 1.0 ChimeraX-WavefrontOBJ: 1.0 ChimeraX-WebCam: 1.0.2 ChimeraX-WebServices: 1.1.5 ChimeraX-Zone: 1.0.1 click: 8.3.3 colorama: 0.4.6 comm: 0.2.3 contourpy: 1.3.3 coverage: 7.13.5 cxservices: 1.2.3 cycler: 0.12.1 Cython: 3.2.4 debugpy: 1.8.20 decorator: 5.2.1 docutils: 0.21.2 executing: 2.2.1 filelock: 3.19.1 fonttools: 4.62.1 frozenlist: 1.8.0 funcparserlib: 2.0.0a0 glfw: 2.10.0 grako: 3.16.5 h11: 0.16.0 h5py: 3.16.0 html2text: 2025.4.15 httpcore: 1.0.9 httpx: 0.28.1 httpx-sse: 0.4.3 idna: 3.13 ihm: 2.2 imagecodecs: 2024.6.1 imagesize: 2.0.0 iniconfig: 2.3.0 ipykernel: 7.1.0 ipython: 9.9.0 ipython_pygments_lexers: 1.1.1 jedi: 0.19.2 Jinja2: 3.1.6 jsonschema: 4.26.0 jsonschema-specifications: 2025.9.1 jupyter_client: 8.8.0 jupyter_core: 5.9.1 kiwisolver: 1.5.0 line_profiler: 5.0.0 lxml: 6.0.2 lz4: 4.3.2 Markdown: 3.8.2 MarkupSafe: 3.0.3 matplotlib: 3.10.7 matplotlib-inline: 0.2.1 mcp: 1.18.0 msgpack: 1.1.1 multidict: 6.7.1 narwhals: 2.20.0 ndindex: 1.10.1 nest-asyncio: 1.6.0 netCDF4: 1.6.5 networkx: 3.3 nibabel: 5.2.0 nptyping: 2.5.0 numexpr: 2.14.1 numpy: 1.26.4 OpenMM: 8.4.0 openvr: 1.26.701 packaging: 25.0 ParmEd: 4.2.2 parso: 0.8.7 pep517: 0.13.1 pexpect: 4.9.0 pickleshare: 0.7.5 pillow: 11.3.0 pip: 25.2 pkginfo: 1.12.1.2 platformdirs: 4.9.6 plotly: 6.7.0 pluggy: 1.6.0 prompt_toolkit: 3.0.52 propcache: 0.4.1 psutil: 7.0.0 ptyprocess: 0.7.0 pure_eval: 0.2.3 py-cpuinfo: 9.0.0 pybind11: 3.0.1 pycollada: 0.8 pydantic: 2.13.4 pydantic-settings: 2.14.0 pydantic_core: 2.46.4 pydata-sphinx-theme: 0.17.1 pydicom: 2.4.4 Pygments: 2.18.0 pynmrstar: 3.5.1 pynrrd: 1.0.0 PyOpenGL: 3.1.10 PyOpenGL-accelerate: 3.1.10 pyopenxr: 1.1.4501 pyparsing: 3.3.2 pyproject_hooks: 1.2.0 PyQt6-commercial: 6.10.2 PyQt6-Qt6: 6.10.1 PyQt6-WebEngine-commercial: 6.10.0 PyQt6-WebEngine-Qt6: 6.10.1 PyQt6_sip: 13.10.3 pytest: 9.0.3 pytest-cov: 7.1.0 python-dateutil: 2.9.0.post0 python-dotenv: 1.2.2 python-multipart: 0.0.27 pyzmq: 27.1.0 qtconsole: 5.7.0 QtPy: 2.4.3 qtshim: 1.2.2 RandomWords: 0.4.0 referencing: 0.37.0 requests: 2.32.5 roman-numerals: 4.1.0 rpds-py: 0.30.0 scipy: 1.14.0 setuptools: 80.9.0 sfftk-rw: 0.8.1 six: 1.17.0 snowballstemmer: 3.0.1 sortedcontainers: 2.4.0 soupsieve: 2.8.3 Sphinx: 9.0.4 sphinx-autodoc-typehints: 3.6.1 sphinxcontrib-applehelp: 2.0.0 sphinxcontrib-blockdiag: 3.0.0 sphinxcontrib-devhelp: 2.0.0 sphinxcontrib-htmlhelp: 2.1.0 sphinxcontrib-jsmath: 1.0.1 sphinxcontrib-qthelp: 2.0.0 sphinxcontrib-serializinghtml: 2.0.0 sse-starlette: 3.4.2 stack-data: 0.6.3 starlette: 1.0.0 superqt: 0.7.6 tables: 3.10.2 tcia_utils: 3.2.1 tifffile: 2025.3.13 tinyarray: 1.2.5 tornado: 6.5.5 tqdm: 4.67.3 traitlets: 5.14.3 typing-inspection: 0.4.2 typing_extensions: 4.15.0 Unidecode: 1.4.0 urllib3: 2.6.3 uvicorn: 0.46.0 wcwidth: 0.7.0 webcolors: 24.11.1 wheel: 0.45.1 wheel-filename: 1.4.2 yarl: 1.23.0 }}} " defect closed normal Structure Comparison can't reproduce all ChimeraX